In Confidence, Stage I
by Angry Warrior
Summary: My version of not only how Voyager should have ended, but also how 'Endgame' should have gone.Hope you all Enjoy! Reviews are appreciated. I was told to warn everyone there is a major character death, but its not permanent, she'll come back.
1. Introduction

In Confidence Introduction

In Confidence is a story I started writing last year, and it continues. It is separated into four books, and I hope you all enjoy!

AW

The present is now the past is then The future is yet to come

Unless...

Time's Cruel Mistress Intervenes

The past is the now The now is the future The future is uncertain...

The people forever forgotten The places never seen The events yet to come...

AW June 2007 


	2. Chapter 1

Part I Rated: M By: AW

Disclaimer: I don't own the people or the episodes but the story is mine.

The darkness surrounded her, and she just waited. It had been three hours since her crew had arrived in the Alpha Quadrant. She stared out at the landscape that was San Francisco from the silence of her room, and just waited.

As she always did, she had insisted that the rest of the crew get checked out, and debriefed before her.

And so she waited.

There was a knock on the door of the small room she occupied. Chakotay walked into the room looking at her silently.

"Kathryn, it's your turn." He paused feeling the need to explain himself to her despite everything and in lieu of the years of service he had provided her. "They insisted on full medicals for the entire crew and that had taken longer than expected. I apologize for making you wait so long."

Kathryn laughed. "You make it sound like it's your fault. I'm sure you had nothing to do with it," she paused. "Well I hope you didn't because if you did, be sure I'll find out. I still have my ways Chakotay."

Chakotay smiled: Still the same Kathryn Janeway; Still the same woman, but for how much longer? Would ground bound life change her? The idea of no longer being in the sky, no longer being transported from place to place in a vessel that was for all rights and purposes hers.

Would it change her?

Of course it would. Life changes people in all of the different ways it happens. Life changes people and makes them different people. Kathryn Janeway had changed a lot over the seven years they had been in the Delta Quadrant. So had he; so had they all. And yet she hadn't. In so many ways she was the same Kathryn Janeway, dedicated to Starfleet and all the ideals that it represented.

Even if, when it came down to it, that institution ended up hurting her. He watched her exit the room. This would be some checkup. The Doctor, (their doctor) had, had enough trouble getting her to give in to simple yearly exams. This one was so much more extensive. It was intended to heal all the beatings and batterings her body had taken over the past seven years.

And seven years was a long time for which to compensate for bad health and coffee over consumption. And he knew that she had had her fair share of both during their time in the Delta Quadrant.

All that was left to do was: wait.

Kathryn had not been to Starfleet medical in longer than she could remember. It had been the seven years she had been in the Delta Quadrant, and she couldn't even recall how long it had been before that.

She walked into a large white room and waited. A red-headed Doctor poked her head out of the back room and she immediately identified her as Dr. Beverly Crusher: former doctor of the Enterprise E. Kathryn got up to shake this woman's hand, and Beverly put a hand on her shoulder. "You don't need to get up. I'll get this done and over with as quickly as possible. Your First Officer told me how much you despise doctors, and doctors' visits."

Kathryn turned a dark shade of pink, blushing at the idea that Chakotay had sold her out to the Doctor. "I don't mean to be rude when I say that, I just don't like the things associated with doctors. Needles, checkups, being injured┘because that's normally the only reason I have to be in a doctor's office."

Beverly Crusher laughed. This woman did not seem larger than life, she was just a woman who had been caught in a bad situation and who was finally allowed to let her guard down. "No offence taken Captain, I know a lot of people don't like to visit the doctor. Just sit down and I'll try to make this as painless as possible."

Beverly took out her instruments and started the examination. She recognized the nanoprobes in her bloodstream for what they were: leftovers of a Borg mock-Assimilation. She had read some of the logs the Captain had brought back with her and knew about Unimatrix Zero, and the attempts to destroy the Borg Collective; this woman was ambitious. She scanned her from head to toe, signs of abuse to her body from improper care for so many years were evident. Beverly shook her head, these ▒Captains▓, they were all the same: stubborn. She scanned her and found something very strange though, something she hadn't expected...the Captain was pregnant.

Beverly took a closer look at her scans. This was no normal pregnancy though; this fetus was not only, not completely human, but it was the beginning of a Borg Drone. Had the Collective finally found a different method of bearing their offspring, of bringing more drones into the world?

She had scanned Lieutenant Torres' baby from head to toe and had not seen the same things within the child, but perhaps she had not been looking closely enough or for the right thing. She tapped her commbadge, "Admiral, I'm almost done here with the Captain, is it possible for you to send in Lieutenant Torres and her baby for one more scan?" Beverly knew that this woman - Kathryn Janeway's former Chief Engineer - had also been assimilated...somewhat. This crew had created a very ingenious vaccine that had allowed them to enter the Borg Collective as drones but still keep their individuality intact. It was quite amazing and quite clever. She was awed in some ways by the lengths these people had gone to, to keep themselves alive in the Delta Quadrant. The breakthroughs made by their doctor...or rather EMH, (although after seven years of being online and the mobility he had achieved through the mobile emitter, she wasn't sure that title was appropriate anymore).

Beverly completed her scans, this woman was for the most part in good health. She needed to get more sleep and drink less coffee, but that was true for so many people. She turned to the Captain, "Captain, you are for the most part in good health. More sleep, less coffee, I'm sure you've heard it all before."

Janeway just nodded her head, "Yes doctor, my Doctor, was adamant about downing my coffee intake." She chuckled, "Am I free to go now?"

Beverly looked uncomfortably at Janeway, "Well there is on thing we have to discuss first."

Janeway looked at her confused. "You said I was in good health...what's wrong?"

Beverly drew in a breath not quite sure how to tell this woman who had endured so much in the last seven years, that her life was about to change forever yet again.

Beverly drew in a seep breath, "You're pregnant...but it isn't a normal pregnancy."

Janeway's jaw dropped. "What do you mean I'm pregnant?"

Beverly paused. "Well the child appears to be half human half...must be a Delta Quadrant species, I've never seen this gene sequence before." She stopped momentarily, allowing Kathryn to absorb the news, "But that's not what's so interesting about this pregnancy."

Before Beverly could continue, Kathryn piped in still unbelieving of the facts. "What do you mean I'm pregnant? I haven't been with anyone..." Then Kathryn's brain kicked into gear giving her the only possible explanation, "Jaffin."

Beverly looked at this poor broken woman before her. "What I was saying was, that's not what's so interesting about this pregnancy."

Janeway looked up. "Yes Doctor, what is so interesting that it caught your eye?"

Dr. Crusher, looked to Captain Janeway, "The baby's body is swarming with Borg nanoprobes." She paused, "Unlike in your body where they're dormant, they are quite active in the baby's body. It's almost as if...as if it were a virus dominating the baby's immune system."

Kathryn was speechless. She shook her head. "What about Miral? Is she okay?"

Beverly held her breath, "I honestly don't know. That's why I asked Tom Paris and B'Elanna Torres to come back with their baby. I wasn't looking for that before, and I don't think your Doctor was either. It could have been overlooked."

Kathryn took in a deep breath, "Well then why did you find it in me?"

Beverly Crusher was not above admitting when it was a fluke. "You had a small imbalance in your level of hormones. I assumed given your age," she paused hoping she had not insulted the Captain, "it was menopause related. The last thing I expected was a baby, and a Borg baby none-the-less."

Kathryn covered her face with her hands and resisted the urge to burst into tears. She had to talk to someone; but who? She thanked Doctor Crusher for her diligence and her discretion in not revealing her condition until she had time to get used to her condition herself, and left Starfleet medical, leaving a message to inform her if there was indeed a problem with Miral as well.

Her first instinct was to go to Chakotay, he had been her friend, her confidant and her first officer for seven years, but she knew this would break his heart, and hers. She had figured that maybe when they got home and Voyager was finally a thing of the past, maybe they could get it together and work it through.

But then there was Seven, and now there was a baby. This would change everything.

Her next thought was to go see Tom and B'Elanna, but if B'Elanna had the same problem she did, which was entirely possible, they'd have their own things to worry about.

Then there was Tuvok, who had made his way to Vulcan to get cured by his son and treated with the fal-tor-voh.

Janeway walked through the gardens of Starfleet headquarters contemplating everything. How would she deal with this? Without thinking or realizing what she had done, she ended up outside his door with her finger on the doorbell. Before she had a chance to ring the bell she fled in horror.

There was no way Chakotay would understand...well not until she had figured it out herself. Then she remembered the message that had been transmitted to everyone, from Voyager. Should they need to talk to someone about the horrors of the Delta Quadrant, counselor Troi, of the Starship Enterprise was available 24/7.

It was 0300 now. Whether or not to disturb the counselor at this time of night was something she had carefully considered after hours of walking the Starfleet gardens. She reached Deanna Troi's temporary quarters, the quarters that were available to her while she treated the Voyager crew and rang the chime.

She covered her face with her hands, and waited. The door opened and a very tired looking Deanna Troi appeared. "Captain Janeway!" Troi sounded surprised despite her sleep deprived state. "What can I do for you?"

Janeway held her breath and let it out slowly. "May I speak with you? Or is it too late?" Janeway hesitated, "Never mind I don't know what I was thinking coming to see you at 0300, I apologize for the inconvenience."

Troi felt the pain and confusion permeating the body of the great Kathryn Janeway and knew she needed to talk to someone. Being so isolated for so many years had no doubt left her very self-reliant and with no one to turn to. Deprogramming this woman would be difficult. Teaching her to trust again and that she wasn't alone anymore would be near impossible. Seven years was a long time to forget.

She reached out to Kathryn Janeway, "Captain, it's no problem. Please come in and sit down. I made myself available to your crew 24/7 and that means you as well." Janeway slowly made her way into the Councellor's quarters. Deanna spoke up, "Captain would you like something to drink?"

Janeway just looked up, "Just coffee please...black if you don't mind." Deanna nodded. "No problem Captain."

Janeway looked to this kind woman before her, "Just Kathryn now, please I have been the Captain for too long without letting myself take a break. Tonight, I need to be just Kathryn."

Deanna Troi looked at her, this could be a long conversation. "All right Kathryn, why don't you tell me what's going on. What was so urgent that it needed to be discussed: immediately."

Kathryn sat down on the couch and began the story: How she found out she was pregnant, how this could be a Borg child, how it was against her moral ethics to abort a child growing inside her.

Finally how alone she felt, since Chakotay had decided that he was going to date Seven: her protИgИe and the closest thing she had thought she would ever have to a child. She began to cry silent tears that had not been allowed to escape since before she had been stranded in the Delta Quadrant, and all of a sudden Deanna was glad that she had chosen to answer the door.

Because this woman definitely needed someone to talk to, and a shoulder to cry on.

Deanna looked at her. Now she had the background behind her peril, now the question was what did she want to do about it? "What do you want to do about everything Kathryn? You've told me about how it happened, about Quarren and the reason you are with child right now." She paused and looked deep into this woman's eyes. "The question is what do you want to do?"

Kathryn paused, thinking about it. Then she turned towards Deanna Troi, "Honestly...I don't know."

Kathryn spoke to Deanna for a while longer, trying to sort through her doubts, her feelings of dread, her un-requited love for her commander.

So many things: so little time.

By the time sunrise came, Kathryn was talked out. The good thing about this conversation was the confidentiality issue. Nothing said to either Deanna Troi or Beverly Crusher could be repeated without her express permission.

Somehow that didn't make her feel any better.

She knew that she could get rid of her problem, before anyone even knew she was pregnant.

No baby: No problem.

But she couldn't do it. No matter what, it wasn't this child's fault, and she couldn't go ahead and end a life for her own convenience.

She had to stay in San Francisco, just for a few more hours, there was going to be a ceremony where all the promotions would be put forth. She had recommended all of her senior staff to go beyond where they were, and many of the junior officers as well.

A few more hours, then she could go to Indiana, and then the explanations would really have to begin. Her mother would no doubt have questions.

Then she thought about Chakotay, he deserved to hear this first hand too, he had been her best friend for far too long to hear it through the grapevine.

After the ceremony, she would divulge her secret; but she didn't want to tell Seven. She had to get him alone.

He owed her at least a couple of hours, after all she had given him seven years of her life. He owed her at least that much.

At least she hoped.

TBC in part II 


	3. Chapter 2

Part II Rated: M By: AW

Disclaimer: I don't own the people or the episodes but the story is mine.

Well it was almost noon. The last day she would have to stay in San Francisco. The ceremony was scheduled for 1 pm, and after that, they would all be set free (including the former Maquis, which had been a point of some contention at first,) until re-assignment.

Kathryn met up with Chakotay and Seven before the ceremony. "Well this is it then; Our last day as members of the Voyager crew."

Chakotay turned to Kathryn, "I'm sure your next crew will be just as dedicated and as devoted to you Kathryn." Kathryn playfully swatted Chakotay on the arm, "I can only hope for a new crew as good as this one was."

The glares that she was getting from Seven would have melted the snow on the Vulcan polar ice caps. "Captain, the Commander and I have some business that we need to attend to."

Janeway nodded and pointed towards the tables that were designated for the Voyager senior staff, and their families. "I'll see you after the ceremony then Commander, Seven."

They both nodded and made their way to the tables they were assigned. Janeway saw Tom and B'Elanna and made her way over towards them and little Miral. She hoped everything was okay with the new baby. "Hello Lieutenants."

Tom saw his former Captain and a smile lit up his face. "Well Captain, you did it: We're home. And what a good job you did of it too."

B'Elanna just laughed, "Oh come on Tom it wasn't all her doing, I had something to do with it too. Someone had to run the engine room."

Janeway smiled, "Do you mind if I sit with you?"

Tom turned to B'Elanna with a look that asked, Do you know what's up? B'Elanna just shook her head slightly. Tom tried to open up to the group, "So Captain, I thought you were going to sit at the head table with Commander Chakotay."

Janeway looked slightly dismayed, "No I gave up my seat to Seven, she wanted to sit with the Commander. It's been that way ever since they became an item." She looked down at her hands mournfully.

Tom piped up trying to break the awkward silence, "Looks like the ceremony goin to start soon." Kathryn turned to Tom about to make some comment about ceremonies and him probably being the next Admiral Paris, and she thought better of it. Tom saw her hesitation and knew she was about to say something, and decided against it. "Hey Kathryn, maybe you'll be the next vice-admiral," he smiled and Kathryn just looked away, loosing herself in the moment, in thoughts of Chakotay and the future they could have had if only she has let him in a little earlier.

She looked back up into Tom's face, "I'm sorry what was it you were saying?"

"Nothing important, you looked a million miles away."

She sighed, "No only about 70,000 light years." And she left it at that. The Paris couple looked at each other then to her.

B'Elanna looked at her daughter in the carrier next to her. "I need to go and change her, I'll be right back." Tom nodded and Kathryn just looked passively on as if she had not even heard what they had said.

With B'Elanna gone to change Miral, it gave Tom an opening to talk to Kathryn. "So Captain, what's up with you?" He paused, gageing her reaction. "We had to take the baby back in and they checked her out one last time, something about hoping there were no nanoprobes from B'Elanna's mock assimilation in the baby's bloodstream. Weird they didn't pick that up before, or think of it. Unless someone else had the problem and they had to make sure it wasn't the same case with Miral."

Kathryn awoke from her daze, more surprise showing on her face than she liked. "What did you say Tom?"

Tom looked at Kathryn an idea forming in his head. He was thinking maybe Seven was pregnant and having some problems, but could it be Captain Janeway? "I said...never mind. It wasn't really important."

Kathryn looked at Tom, she pulled him aside. "Come here Tom, let's go talk outside for a minute." She pulled him all the way outside to the grounds of Starfleet Academy. Away from prying eyes, and listening ears.

She looked him in the eye and all Tom could think was this fiery woman was the Kathryn Janeway they had all known and grown to love. "What I say to you now, you can't repeat Tom." She paused, "Well I know B'Elanna will hear it, but you guys have to keep this to yourselves. I haven't had a chance to talk to Chakotay yet. I know right now he's not too interested in me, but I also think it would hurt him if the news didn't come straight from me."

She began to tell her tale. How she was pregnant, the possible problems with the nanoprobe technology still swimming inside of her. The fact that Jaffin was the father, and she had no way to tell him, or to even justify having an affair while in the Delta Quadrant. Her worries about what could be wrong with this child, about what would happen, and if this child would just be a thing of study for Starfleet.

Finally her aversion to abortion and how she could not end an innocent life, no matter what. "So Tom, now you know. Please keep this to yourself. I have no interest in overshadowing the crew's accomplishments, or being the center of attention at this time. As I said before, I haven't talked to Chakotay, I haven't told my mother, my sister...Oh god I can't do this."

Tom looked at her, Kathryn Janeway one of the strongest women he knew, and here she was breaking down right in front of him. He pulled her to a hug of comfort. A hug that said I will always be here for you, all you have to do is ask. "Captain...Kathryn, I'm sure B'Elanna and I can take you in for a few days; I'm sure you'd like to visit your goddaughter and your namesake."

Kathryn looked up surprised, her problems momentarily forgotten. She gave Tom a puzzled look.

Tom piped up. "Her name is Miral Kathryn Paris." Janeway had tears of joy running down her cheeks. If she could forget this for one day, it might make it all better.

She looked to Tom, thinking of the ceremony about to start: "We'd better get back inside. They're probably ready to start the ceremony, and wondering where the hell we went." Tom laughed, "Yeah they might think I ran away with you and we had a wild passionate love affair."

Kathryn smiled, "Unlikely, but I guess it▓s possible."

They went inside and greeted the many Voyager people. Had the room ever filled up in the fifteen minutes while they were outside airing Kathryn's dirty laundry. Kathryn approached the table where B'Elanna and Miral were sitting. "Sorry B'Elanna, I needed to borrow your husband for a minute. I brought him back for the most part no worse for wear."

B'Elanna laughed, "I hope so Captain, I didn't want to have to blame you for a failed marriage and a broken home."

Kathryn excused herself and made her way over to the table where the couple of the hour sat: Commander Chakotay and Seven of Nine.

B'Elanna looked at Tom, "Is she okay?"

Tom shook his head not sure what to say, "I hope so B'Elanna." He paused, "I hope so."

Kathryn approached the table and Seven looked up to see the woman that was her competition, and always would be. "Captain." Janeway nodded, and approached Chakotay. Seven piped up, "I am going to get a drink for myself and the Commander, would you like something?" Even though her words were nice, there was an acidity to her tone of voice.

"No, thank you Seven, I'm fine."

Seven nodded and made her way to the drink stand. Chakotay moved over a seat and made room for his former Captain. "Kathryn, nice to see you again." He paused, "I need -"

"I - " Kathryn said at the same time. Kathryn nodded at him. "We need to talk. You free for coffee after the ceremony?"

Chakotay smiled, "I think I can manage to fit you into my schedule." He opened an imaginary planner, "I'm free after the ceremony and most of the night is clear."

Kathryn couldn't help but chuckle. "Alright then, how about four o'clock. The little coffee shop just across from the flight school."

Chakotay nodded, "You know Kathryn you don't have to leave so soon, you can sit with us."

Out of the corner of her eye, she saw Seven scowling at her. "No, that's okay. I have a seat next to B'Elanna and Tom, I haven't really gotten the chance to spend much time with them, or get acquainted to Miral Kathryn."

Chakotay looked at Kathryn, "Well they made a good choice of a middle name, and godparents for that matter."

Kathryn smiled, "Who did they make godfather?"

Chakotay grinned back, "You're looking at him."

Kathryn laughed, how ironic life was in so many ways. She looked up just in time to see Seven ready to sit down. "Excuse me Captain. That is my seat."

Janeway looked at Chakotay and rolled her eyes. She watched him mouth the words, We'll talk later.

Kathryn went to sit down, and the awards ceremony began. What also began was the most unexpected thing, well to Kathryn anyway; Janeway had been promoted. If only they knew.

She heard Admiral Paris' voice. "This is a bit impromptu, but it's the best we could do at such short notice, and we certainly didn't want to wait. Captain Janeway, please step forward." Kathryn did as she was told, hoping this wouldn't be a dressing down. "For your determination in getting your crew home despite almost impossible odds-and for beating the Borg at their own game-you are hereby promoted to Admiral."

She looked away, did not want to look people in the eye. But she knew that her promotion to Admiral meant no more space travel, no ship of her own, and life as she had lived it, (for the past almost fifty years) was over. Kathryn went back to sit down at the table with Tom and B'Elanna. Slowly each ensign and lieutenant that deserved to be promoted made their way up to stand in a line before Admiral Paris. Both Lieutenants Paris and Torres became lieutenant-commanders. And Kim, Vorik and Campbell turned to face the applause as lieutenants. Kathryn, Admiral Janeway now, looked down at her hands. At least most of her crew that deserved promotions had gotten them.

Kathryn sat through a dinner banquet she had not enjoyed and simply tolerated the congratulations and the applause with a kindness and a smile she had learned over the years to produce on cue.

After the all too long banquet, about 2:30┘ Kathryn went to Indiana. It was time for some explaining, and she was in no mood to face the music alone.

The transporter took her away from the Starfleet politics, the promotions: a life she had lived for far too long. She had told her mother and her sister not to come to the banquet, she had told them that she would meet them directly afterwards at home. She saw her childhood home in the background, and began the walk, the walk that was her last one so problem free, for the rest of her life.

Kathryn approached the door and went to knock, just as the door opened and she was just about bowled over by her overanxious mother and sister. "All right, all right: Nothing overly special to see here, just me."

Phoebe pulled the jacket off of her sister. "Oh Kathryn, you look good, a little too skinny mind you... but you were always the twiggy one." Kathryn returned her sister's hug, it was good to be home. It all seemed surreal, they had been in the Delta Quadrant for seven years but they were finally home.

They entered her mother's home and went to sit down on the couch. Her mother piped up. "Kathryn, tell us all about it. Seven years was a long time to be alone. I hope you're happy Kathryn."

"Well it was a long strange trip, but I'm just so happy to be home."

Phoebe piped up, "The Captain that brought Voyager home."

Kathryn stopped her right there. "I didn't do it alone... I had a lot of help from everyone. And it▓s no longer Captain, as of today you are speaking to Admiral Janeway."

Gretchen looked at her daughter, "Oh Kathryn, that is such good news. You won't be on the road for months at a time, maybe you'll finally have a chance to find a good man and give me the grandchildren I've wanted from you for so long." She winked playfully Kathryn's way.

Kathryn looked at her mother. "That's what we need to talk about mom."

Both Gretchen and Phoebe's jaws dropped. "Have you already made me a grandmother, possibly with that handsome first officer of yours?"

Kathryn shook her head, she wished. "No mom, that's not it at all." She paused, "I'm pregnant mom."

Gretchen took Kathryn in her arms, "Kathryn that's wonderful. Someone will take on the Janeway bloodline after all." Kathryn sighed, "Its half Borg mom. I don't know what to do. Her father is an alien from another quadrant that I got together with under mind control. It's not exactly the picture perfect way to bear a child."

Phoebe could see that her sister was distressed. "Kathryn, we'll love this child no matter what, and so will you. You know that." Phoebe embraced her sister in a hug that spoke volumes.

"Does anyone have any idea what time it is?"

Phoebe looked at the chronometer on the desk behind her. "Just about 1530 hours Kathryn, almost three thirty."

Kathryn did a double take. "I have to make my way back to San Francisco. I have to meet up with someone."

Gretchen moved up to Kathryn, "It wouldn't by any chance be that dashing first officer of yours would it?" Gretchen could have sworn Kathryn blushed but said nothing.

Kathryn looked at her mother. "Wouldn't you like to know. I see nothing has changed: You▓re still trying to get your nose in my social life." Gretchen laughed, "Would I be your mother if I didn't?"

Kathryn looked at her, "No. But I'm still not telling you who I'm going to see."

With that final thought Kathryn left her mother's house and made her way to San Francisco to meet Chakotay and explain a few things.

Back in San Francisco, Chakotay sat in the cafИ with Seven. He had to end this, it just wasn't real enough. She had the emotional level of a teenager just learning about love and live. He couldn't deal with it. He was over 50 years old, too old to teach her the ways of the world. He wanted so many things in life, love, a family, a house to call his own. None of these things would happen with Seven: None of them.

He took Seven's hand. "Seven, I like you, and I respect you, but this isn't the type of relationship that can keep on going." He looked at the emotions as they ran across her face. "We have to end this, before we get too close and the pain is just too much, and time is wasted. I can't wait any longer. I waited for Kathryn for years and she just didn't want to have anything to do with the notion of perhaps being perfect for me, and if I want all these things I described, I need to try to find it." He got up and kissed Seven on the forehead. "Thank you, for being there for me in the Delta Quadrant, and maybe for being my soul mate in a different life, but in this time, this life: it's not meant to be." He walked out of the cafИ and left Seven alone to ponder her life choices.

It was almost 1600, and he was off to see Kathryn. Maybe they could make one last go of it, or maybe not. Maybe they were just destined to be friends and nothing more. Or maybe she was destined to marry him and bear his children.

Or maybe they were meant to go their separate ways and part company for good.

Life was funny that way. He arrived at the small coffee house and saw Kathryn sitting there waiting for him, wearing her new uniform and dressed with the pips of an Admiral. Kathryn always Fleet, always working, never on break. He approached Kathryn, "I thought they gave the order for all Voyager crew to take the next month off."

Kathryn smiled, "So they did. I just don't have any other cloths."

Chakotay laughed, "So what was it that was so important that you had to see me right away?"

Kathryn opened her mouth to answer him and it all went black as she lost consciousness and the darkness enveloped her.

TBC In Confidence, Part III 


	4. Chapter 3

Part III Rated: M By: AW

Disclaimer: I don't own the people or the episodes but the story is mine.

The surroundings seemed familiar. Like a dream that should have lasted forever. The water, the sun, the house. It looked like New Earth, it felt like home.

Where was home? Her thoughts moved to Voyager, she saw Voyager, what could have been, what was, what could be?

Then it all went foggy and all of a sudden she saw the wolf, then the lizard. The sun was gone and the warmth disappeared. She was in a cold, cold place.

It felt wrong, yet it felt familiar.

Life as it was, as it should be and as it would be.

Chakotay looked horrified as Kathryn's body appeared to go limp and the life seemed to drain out of her. Oh my god, not Kathryn.

Chakotay screamed out to anyone who would listen. "I need some help here. She just collapsed." No one was listening, why was no one doing anything. "I need some help. Can someone please contact Starfleet Medical, Admiral Janeway just collapsed."

All of a sudden people sprang to life. The mere mention of the 'Delta Darling' made people move just a little faster. A voice from behind made him jump, "I've contacted Starfleet Medical, someone will be here as soon as possible. They've already dispatched emergency rescue teams."

Chakotay approached Kathryn and lifted her lifeless body into his arms. He had to do something.

But all he could do was wait. Wait and pray for the best possible outcome: A life with Kathryn Janeway at his side.

Beverly Crusher was told to be ready for a medical emergency that should reach Starfleet medical and her temporary post in less than ten minutes. Emergency crews had been dispatched and she had no idea what the problem was. Just that one of the former Voyager crew was in trouble and had been immediately dispatched to her. She had just checked out the whole Voyager crew though, and barring Captain, no Admiral Janeway's condition nothing out of the ordinary had come up.

She just hoped she hasn't missed something serious in the examinations. They had after all been subjected to many Delta Quadrant diseases and parasites and so on, and some of them of course, were probably not even detectable by Alpha Quadrant standards.

Alpha Quadrant, Delta Quadrant, Gamma Quadrant, it all made medical science quite confusing. There was just too much to remember, too many things to know.

She turned away from the postulations of what it could be and set up for the new patient, whomever that may be.  
And so Beverly waited.

At the coffee house Chakotay watched the medics from Starfleet medical make an examination of Kathryn Janeway. Her heartbeat, her breathing everything seemed okay. But her blood pressure was low...why he didn't know. "Sir we need to bring her back to Starfleet Medical. We'll contact you as soon as we know what's going on."

Chakotay got angry, "The hell you will. I want to come."

The medics looked at each other, with looks that said 'this guy has it bad' and finally agreed. "Fine, but you have to stay out of the way."

And in an instant the coffee house was gone and Starfleet medical had appeared in its place.

Beverly Crusher, now a Commander, appeared from behind the door and looked at the unconscious body of Kathryn Janeway. She approached the patient and ordered her taken to a room behind the door. The magical door, where all medical personnel took their patients.

The door where miracles happened and tragedies unfolded and situations became better or worse in the blink of an eye.  
So he sat and waited, the story of his life: Sitting and waiting.

Beverly looked at this woman. She had been checked over earlier that day and there had been no problems. But it was common among human pregnancies to cause light-headedness and even fainting.

She studied Kathryn's blood pressure. Definitely too low, but here there was something else interesting. Apparently, the pregnancy had re-activated the nanoprobes in Kathryn's blood. Oh god, this was going to be trouble.

Beverly immediately started shouting out instructions. "I need a containment field around her. I need to know who she's been in contact with and I need to have them all checked out. If the Borg have altered the nanoprobes to act like a virus, in theory they could be transmitted like a virus; I need to know!" She paused and looked at all of her colleagues. "All of you have been subjected to this woman. I need you all to get yourselves checked."

One of the ensigns turned to look at Beverly. "Dr. Crusher. Isn't this the same Kathryn Janeway that just returned from the Delta Quadrant?" He watched Beverly nod her head, "In that case don't we have to alert everyone who was at the banquet? Her family. The people she has been in contact with, her former crew."

Beverly felt a headache coming on. The ensign opened his mouth again, "And didn't a gentleman bring her in?" Beverly bowed her head, how much did this man know? Did she have a right to tell him if Kathryn had not had the chance? Could she afford not to tell him? Beverly had some thinking to do. "First of all get him into isolation, don't tell him anything I'll speak to him in a couple of minutes. Stabilize the Admiral pronto. We'll worry about the possibility of spreading this virus. If it is a virus after that."

Beverly Crusher watched the people around her begin to work. These were the best Starfleet had to offer and she still wasn't sure they could fix this problem.

Perhaps the Borg had finally managed to do what they had wanted to do for years, assimilate species 001.

Beverly looked at the books behind her and spread them out before her. She opened up the first book she'd need to consult to begin this process of hopefully creating a vaccine to combat this threat to Earth.

She had to get in touch with Starfleet Command, at the highest levels; this had to be fixed.

Beverly entered the room where Admiral Janeway lay. "Okay people, what have you found? What's going on?"

One of her Lieutenants came forward. "She appears to be in no danger, but the rate at which the nanoprobes are spreading is incredible." She paused for a second, "I think though, the most interesting thing is, she is not being completely assimilated."

Beverly thought, "Theories people?"

The Lieutenant piped up again, "I think maybe it would be prudent to get the doctor on Voyager involved. He has had the most experience with the Borg, completely and incompletely assimilated. He created the vaccine that made them immune to joining the hive mind, but still let them get 'assimilated' to a point."

Beverly got comfortable with the idea, "That's actually a great idea. Who else would know more about this, or about Kathryn Janeway's health for the past seven years for that matter..."

"Commander, I think she's waking up."

Beverly turned around to the frightened eyes of Kathryn Janeway. "What happened? Why am I back at Starfleet medical?"

Beverly walked up to Kathryn Janeway, "Don't worry. We have it all under control. The nanoprobes are spreading at an astronomical rate throughout your body. The child you're carrying apparently triggered a response in the previously dormant nanoprobes." She paused, "but that's not the most amazing thing..."

Janeway was shaking her head confused, "Just cut to the chase doctor. What's going on?"

"We're not entirely sure Admiral. The nanoprobes are attacking your body, as a virus invades an infected person's bloodstream. The problem is... we don't have a vaccine for this virus and we're not even sure if it can be spread by you"  
Kathryn was horrified by the fact that she had possibly infected all the people she loved, the people she had spent the last seven years with, as well as the people who had waited seven years for her. "Doctor, what are the chances that others were infected?"

"I'm not sure Admiral, but I suggest that if you haven't told that man who came in with you and who is now sitting in isolation, that you explain to him why he has been forced into decontamination."

Oh god, Chakotay. She looked at Beverly Crusher. "May I go and visit his holding area? I need to speak to him before he hears this second hand."

Beverly looked at Kathryn. "Of course, but make it quick, I want to try and get this cure and vaccine hunt underway as soon as possible."

Kathryn looked at her, "Understood doctor. I'll make it as brief as possible."

The doctor looked over to one of her assistants. "Can you please show the Admiral where Commander Chakotay is being held"  
The ensign nodded, and helped Kathryn into the wheelchair. Kathryn felt she was perfectly capable of walking, but the doctor had insisted. She was pushed down the hall and led into a room, where Chakotay was supposedly being held.

The door opened and the assistant turned to Kathryn, "If you need anything, just buzz us through the panel on the wall." Kathryn nodded, as the door closed behind her.

Chakotay slept facing the wall, looking like an angel. Kathryn was almost remiss in disturbing him. "Chakotay." She approached him, slowly shaking his arm. "Chakotay?"

Chakotay recognized the voice of Kathryn Janeway before he had a chance to turn around and see her. When he finally turned around he saw her in the wheelchair and was horrified. "What's happened to you Kathryn?"

She looked at him, "I wanted to tell you earlier Chakotay. I wanted to tell you everything, but the time never seemed right. You were with Seven, and you seemed to be so happy..."

Chakotay looked at her, and realized she refused to look him in the eyes. He reached out and tipped her chin up so she was forced to do just that, stare into those obsidian orbs. "Kathryn, it's over."

Now it was Kathryn's turn to look surprised. "What happened?"

He shook his head, "It just wasn't right. I realized I will never love someone else the way I love you, and I couldn't stand to put anyone else through a love that wasn't complete."

Kathryn just stared at him. "I have to tell you something Chakotay."

He looked at her prompting her to reveal her secret. When she didn't answer he verbalized his question. "Kathryn what is it"  
The tears continued to pour down her face. "Chakotay... I'm pregnant."

His jaw dropped and he was angry and happy and confused all at the same time. Happy that she would finally have the child she had wished for all her life. Angry he has not been able to be the one to father it himself.

And finally, confused: Confused that he had not been a good enough friend to know what was going on in her life. He had missed out on a part of her life, and for that he would never forgive himself.

TBC in part IV 


	5. Chapter 4

Part IV Rated: M By: AW

Disclaimer: I don't own the people or the episodes but the story is mine.

Chakotay watched as the woman he has come to know and love told him of her impending motherhood. The love of his life had found someone else. He looked up and realized Kathryn had been talking to him the whole time and he hadn't heard a word she'd said.

"...Jaffin and I, it was a fling in the...Chakotay? Chakotay!"

Chakotay awoke from his mind's games and stared at her. "I'm sorry, I didn't hear what you said. I wasn't listening. After the words, 'I'm pregnant' my mind seemed to wander."

"This baby. It's Jaffin's." She held her breath while she waited for his response.

"Jaffin?" He searched his mind and his memory for the name. Who was, "The man from Quarren?"

Janeway nodded. "I didn't even know who I was. If I had, I never would have moved in with him, and I surely would have been more careful when it came to birth control..." She paused, "I don't remember much of it, I just remember I thought I was happy. And then I found out when I got back, after the ordeal with the Borg Queen here on Earth, and our last real mission as a 'Voyager Crew' that I was pregnant. I did a lot of soul searching and I can't terminate this life Chakotay. It's not her fault. It's not my fault, it's not anyone's fault: It just is."

Chakotay drew her into a hug. "I'm so sorry Kathryn, I had no idea..."

She shook her head. "Neither did I." She held onto him for dear life, then she backed up. "I do need to tell you one thing. Remember Unimatrix Zero, and the time we were all partially assimilated? This baby is swarming with Borg Nanoprobes. They don't know what's going on. It just began activating nanoprobes in my body, that's why they might check you closer than usual. This thing is acting, in my body: like a virus and we have no idea why...or if it's contagious, or if it's remnants of the Virus we dealt with, with the Queen and thought we'd destroyed...we have no idea."

Kathryn was crying at this point. Not sure what her life would be like with a half-borg baby, without a father to give her the support any new mother needs. "I don't know what to do Chakotay."

Chakotay reached up and wiped the tears from her eyes. "Kathryn listen to me," he tilted her head up so she was looking right at him. "I will be here for you, no matter what and I just want you to know that." He pulled her to him, "You did what you had to do in the Delta Quadrant. No one could have known what the future would hold; No one could have guessed that this would happen. I love you Kathryn. I need you to know that you'll never be alone: As long as I walk this Earth."

An intern interrupted their meeting. "Admiral, I need you to come back to your room. We need a list of all the people you've been in contact with since you came back from the Delta Quadrant, I'm sorry to bother you but it is of the utmost importance."

Janeway nodded. "I understand." She turned to Chakotay, "We'll talk later. I promise." She let a laugh escape, "Hell we could both be locked up here for a long time."

Kathryn's mood quickly changed. "Well I'd better get to the other side of the medlab. Someone wants to look me over. That's all I need another doctor bothering me about caffeine intake..."

Chakotay took her hand and squeezed it in a manner that was a little beyond best friends. "Hopefully everything will be okay and I'll see you and the little one in a little bit."

Kathryn let her hand drop to her abdomen. "Yes, hopefully."

With that thought she walked out of his room and back to her own captivity.

TBC in part V 


	6. Chapter 5

Part V Rated: M By: AW Disclaimer: I don't own the people or the episodes but the story is mine.

Kathryn arrived in her room at Starfleet medical to the stern look of Doctor Crusher. "Admiral, I understand that there is a long history between the two of you, but I need to know who you've been in contact with since your return. According to these scans, Commander Chakotay and your mother and sister show no signs of the infection. I have no idea why it has targeted you, but you don't appear to be contagious. I checked out lieutenants' Paris and Torres' baby and she shows no signs of it either and B▓Elanna was involved in the assimilation scheme with you two years ago."

Kathryn nodded. "According to your scans though, there is no threat to anyone's health that I come in contact with, correct?"

Beverly looked at the Admiral. Not that I can see, but I want you back here in a week's time. I'll be the one who takes over your prenatal appointments now." She paused, "And by the way Admiral, you really should gain some weight, eat properly, sleep more, according to these scans you're the equivalent of four terrain months pregnant. You should have more to show for it by now."

Kathryn nodded. "Understood doctor, I'll try to have more to show for this pregnancy in a week's time. Are Chakotay and I dismissed?"

Beverly nodded. "For the time, but if you have any symptoms, I expect to see you immediately."

Kathryn nodded and made her way back to Chakotay's 'chambers'.

She quietly stepped into the room and looked for Chakotay who was slumbering near the far side on the cot. "Chakotay, we've been released."

Chakotay slowly made his way from the land of sleep to the land of the waking. "Kathryn?" He shook the cobwebs out of his head. "Is everything okay with you?"

Janeway nodded. "As far as she can see, but I need to come back in a weeks time. She's taking over my prenatal care"  
Chakotay nodded and led her out of Starfleet medical. "What do you say we go and get something to eat. You're still awfully scrawny, you could probably use a good meal or two."

Kathryn gave him a death glare. "I suppose you're right. Let's go."

The former Command team ended up at a small Bajoran restaurant on the grounds of Starfleet Command. They had a nice meal and then proceeded to Chakotay's quarters on the grounds of Starfleet headquarters.

They sat and stared at each other. They both had some explaining to do, and neither knew where to start.

Chakotay broke the silence with the subject both had been avoiding and neither wished to broach. "So, how far along are you"  
Janeway stared at the ground, unsure of what to say. "The doctor guesses me at about four months... but she wasn't sure seeing as we've never even had contact with the species let alone interspecies breeding."

Chakotay looked at her and clasped her hand. "Kathryn, I know this is hard for you, but you have to take better care of yourself and decide what you're going to do about it."

Janeway looked at him incredulously. "What I'm going to do about it? I guess I'm going to have a baby." Her flippant remark hurt his feelings.

"You know that's not what I mean Kathryn. I'm willing to help you deal with this, but you have to let me in."

Kathryn bowed her head and began to let the tears fall again. "For everything I planned when we got home, it didn't include this. I always assumed if and when I did decide to have a baby I'd have some control over it: here I have none." She looked out the window in the living room and essentially ended the questioning...

Starfleet Medical 0300 hours

Seven of nine lay on the bed, waiting for the tests to finish. Having had contact with Admiral Janeway, and having been part of the collective herself she was a critical part of the investigation into Kathryn Janeway's condition.

The Admiral was pregnant carrying an apparent half Borg child. How this came to be and why she was such a big part of the investigation was beyond Seven but she had been a large part of everything Starfleet since arriving in the Alpha Quardrant.

She remembered the offer of the pseudo-Borg-Queen, begging her to take over the drones on Earth. She remembered the temptation, the sorrow she felt for this woman who had endured so much.

She remembered...

An adult Brenna Covington stood before Annika now. She reached out and clasped Annika's hands, two tall, fair-haired women, so similar and yet so different.

"Take it," Brenna implored. "Take it. Take them. You know what I have endured. You know what I feel for them. They need a queen. They need you. You can be better than the original queen. You can exceed the programming. You can look at your drones as beloved children, not as things to be used and discarded. They can be glorious. You can take them to perfection. There's nothing they and you won't be able to achieve."

Annika clutched Brenna's hands. This was no trick, no lie. The Royal Protocol, modified and adapted by Brenna Covington, surged through her. She could feel it already, closing off some parts of her body, opening others, exploring, downloading information. Brenna was right. Already, she could hear the voices of the confused hive, turning to see, seeking solace. She could be a new type of queen, a benevolent, loving monarch, to lead her people to perfection and-

No. She would not be seduced by the glory. Sweet though it was, it was an illusion. The Borg represented suppression of individuality, no matter how the queen thought of her drones. Brenna sensed her decision.

"No," she cried, "please, don't abandon them!"

"I am sorry," Annika said, sincerely, and slowly, deliberately, closed the door on the Royal Protocol, the clamoring of drones, and her last, best chance to be a part of something infinitely greater than herself.

Seven laid in wait, she was receiving something that she didn't understand. It's not over... the files have been downloaded, the Queen will live on. Seven didn't understand at first... unsure of what she was hearing, unaware of the importance of the words. Then like a flash of a camera, she understood. The Queen was immortal, so long as she could find someone to take her place, and found someone she had...

Seven opened a comm signal to Starfleet Medical, "Seven of Nine to Commander Crusher. I understand it's late but I have to speak with you. I have something of the utmost importance, new information."

Crusher came on the com line sleep deprived. "What's going on, it's 0315 in the morning Seven of Nine."

Seven impulsively went on. "I need to know the sex of Admiral Janeway's child."

TBC in part VI 


	7. Chapter 6

Part VI Rated: M By: AW Disclaimer: I don't own the people or the episodes but the story is mine.

Seven and Doctor Crusher met at a coffee shop, just outside of Starfleet Headquarters. It was 0430 in the morning and Seven better have something good.

Seven met the doctor there, at the coffee shop, but still did not understand the human need for this caffeinated substance. She knew that when she had been on Voyager Captain Janeway had had an affinity for this drink, but she still did not understand.

No matter, she took the coffee and sipped the bitter substance looking at Doctor Crusher. "The reason that Admiral Janeway is infected and not the rest of the people she has been in contact with, is obvious. Were you involved in the problem with the Royal Protocol and Brenna Covington before her demise?"

Beverly shook her head, "Not directly, no. I was aware of what was going on, but at the time I was assigned to the Enterprise E and didn't have anything really to do with her treatment or the treatment of others infected." She paused, "Every member of Starfleet medical has been thoroughly briefed on it though. I do understand what happened."

Seven sighed, "I still have implants from my 20 years with the Borg. And sometimes I do get messages. Before Ms Covington died, she tried to pass the responsibility of being the 'New Borg Queen' on to me. When I refused I had thought it was all over." She paused unsure of how much she should reveal, "When I discovered the Admiral's condition I was surprised, but it was really no concern of mine. Until last night."

Beverly was puzzled. "What happened last night that you had to inform me immediately, and at 3 in the morning"  
Seven took in a deep breath. "I got a message from the new Borg Queen."

Kathryn had fallen asleep on Chakotay's couch. She awoke to a soft snoring to her left and realized Chakotay had fallen asleep there as well. She had a headache that wouldn't go away. Something she had not bothered Commander Crusher with, as she would have kept Kathryn longer than she wanted at Starfleet Medical. The odd thing was, the pain in her head was slowly making itself sound like a crowd, speaking loudly, incoherently...

She went to get up and noticed that over the past five hours, she had gained what looked like ten, maybe fifteen pounds. She looked pregnant...

All of a sudden out of the crowd of voices, she heard coherently a voice above the rest, It's not over.

The telepathic message that Kathryn was receiving frightened her. Oh god, what have I done?

She looked over to Chakotay and shook the sleeping man out of his slumber. "Chakotay, get up. We need to go to Starfleet Medical. Now."

Chakotay slowly awoke and shook his head. "Kathryn what's..."

He looked at her and realized that she looked like she was about five, maybe six months pregnant now. "My god Kathryn, what happened? You look..."

Her eyes were frightened as she looked at Chakotay. "I know Chakotay. I just got a message. It's not over."

Chakotay led Kathryn out of his apartment and to the transport site.

TBC in part VII 


	8. Chapter 7

Part VII Rated: M By: AW Disclaimer: I don't own the people or the episodes but the story is mine.

Seven and Doctor Crusher made their way to Starfleet medical at the crack of dawn. It was now 5 am and they had finished their coffee while Seven answered all of Dr. Crusher's questions, as best she could (the one's she had answers to anyway.  
When they arrived at Crusher's office, Admiral Janeway and Commander Chakotay were there, Janeway looking more frightened then Seven had ever seen anyone look. She took a close look at Janeway: she looked as if she had gained weight over the last few hours. Beverly walked up to the former command couple and gave a questioning look to Kathryn. She slowly lifted her top and showed a very distended abdomen compared to what she had seen not a day ago, filled with faint blue lines, reminiscent of the Borg assimilation work.

Crusher opened her tricorder and started the scans. "Admiral, we have some serious issues here..."

Kathryn looked to the woman, "I don't want this thing inside me anymore. I know that there are laws against abortions past the first trimester but..."

Crusher shook her head. "Kathryn, I wouldn't do it even if you wanted me to. This child has intertwined herself into your system so intricately, that to remove it might kill you." She paused, "I don't even know what will happen when its time for you to give birth, and considering the current changes, I'm not sure when that will be. According to these scans, you're showing a development of six months."

Kathryn's whole body began to shake as a chill enveloped her and fear took her over. "What is the chance that this child poses a real risk to the Federation?"

Seven of Nine chose that moment to make her presence known. "This is the new 'Borg Queen'. She is Brenna Covington's replacement. After I refused the 'honor' she must have scanned for another willing host. Unfortunately, you're previous 'pseudo-assimilation' and the fact that you were with child, made that baby the perfect choice."

All the color drained out of Janeway's face as she tried to comprehend what Seven was telling her. "Do you mean that this child, I carry: my daughter, is the new Borg Queen?"

Seven nodded. "Yes, Admiral."

It was at that moment that Janeway lost control. "I want it out, I can't give birth to that. I was having a hard enough time accepting the fact that this child was created without my consent, in a world I didn't know; But to know that this would be 'the New Borg Queen', the outcome... it's unacceptable. I want it out NOW."

Crusher shook her head. This woman was nearing hysterics. Not that she blamed her. "I told you, I can't. I have no idea what trying to remove this embryo prematurely will do to you."

Chakotay watched in slow motion as Kathryn collapsed. He rushed to her side as he watched the blue-green veins of the Borg collective begin to snake their way across Kathryn's pale flesh. He looked to Dr. Crusher. "You have to save her."

Beverly shook her head. "I'm not sure how, I'll have to investigate..."

Chakotay shook with rage. "I want you to get our doctor involved. He may only be an EMH, but he has had the most experience with the Borg, if that's the only chance Kathryn has, I want you to take it."

Beverly opened her mouth to protest the Commander's orders, when Chakotay once again took control of the conversation with a passion he hadn't realized he held any longer.

Chakotay was yelling at this point. "I don't think you understand Doctor. I'm not making a request." He drew in a deep breath, "I love her and finally have her, willingly and I need you to find an answer."

Crusher looked at Chakoty. "Commander, if you continue to interrupt my treatments, I will have to ask you to leave. If you wish to stay I suggest you calm down."

Beverly looked down at Kathryn. She had begun to convulse as the lines across her skin grew darker. "I need to get her into surgery now, Commander. I'm sorry. I'll keep you appraised of her condition."

And with that, Chakotay lost sight of Kathryn for the second time since their return to Earth. He remembered his conversations with Seven: He looked to Seven of Nine, "I thought I loved you, but your people, or the people who were 'your people' make me sick." He paused and turned around, "Please go, I can't look at you right now."

Seven turned to leave. She thought that joining the Voyager crew would help her re-gain her humanity, but in reality it had possibly led to their demise. This had to end.

Seven went to the quarters they had assigned to her at Starfleet medical. She went to the medical cabinet and took out a lethal dose of a sedative. She began to feel sleep overcome her. Before she left the world forever though, she left a note for the EMH and a command to activate him in exactly two hours. She felt her breath begin to slow, and her mind begin to quiet.

Maybe in the next life, she would finally find the peace and humanity she had spent her whole mortal existence searching for.

At least she hoped so...

TBC in part VIII 


	9. Chapter 8

Part VIII Rated: M By: AW Disclaimer: I don't own the people or the episodes but the story is mine.

In Confidence Part VIII

Rated: M

By: AW

Disclaimer: Blah blah blah blah, you all know what goes here.

Three days...he didn't hear anything for three days. Not knowing, not having any idea what was going on. Just that Kathryn was in pain.

Chakotay entered the dream world hoping that, that was going to give him some clarity.

All he saw was the stern face of his father, shaking his head: Not really giving any indication as to what was happening.

Then on the fifth day he got a visit. From the Doctor, their doctor.

He opened the door and let the doctor enter. "Doctor, I hope you've come with good news."

The doctor's grim expression left no room for argument. That day he knew that they had lost Kathryn Janeway. Chakotay let a tear fall down his face. "Was it peaceful?"

The doctor nodded. "I kept her out of pain, and let her go peacefully." He paused and looked up into the eyes of his former Commander. "Chakotay, I do need to tell you something though: You have a daughter. It appears that on Voyager, the agreement you made, that should anything happen to either of you, the other was responsible, is still binding."

Chakotay felt the color drain from his face. "I have a daughter?"

The doctor nodded. "We thought we'd hear from you before now, but I know this has been a trying time for you."

Chakotay just nodded. "Can I pick up our daughter then?"

The doctor looked a little unsettled. "There is one problem though Commander. This baby was born - as Seven told us - the 'New Borg Queen'. You've heard of the new outbreak of the Borg Virus, the virus that was started by Brenna Covington? Well the messages appear to be coming out from Starfleet Medical; this child is sending out messages. Starfleet will not allow her into the mainstream population: They fear her."

Chakotay shook his head. "Why did you come and tell me this, if there's nothing I can do?"

"Well there's the glitch: You are this child's legal guardian, so you are allowed to have contact with her. Although you are the only one. And you must go alone."

Chakotay was still trying to comprehend what the doctor was saying. "So I can go and get attached to this child, but not ever be allowed to give her a fair chance to live?"

The doctor shook his head. "I don't think you understand the seriousness of this situation. This child is the Borg Queen. Kathryn Janeway destroyed one, and spawned another, so to speak."

Chakotay did not look amused at the doctor's attempt at humor. "This is the last thing I have left of Kathryn, and you're making jokes?!"

The doctor looked sternly at Chakotay. "I'm not making a joke. This child could be the end of the Federation, and of all of our lives."

Chakotay decided to let that go. "Alright, well where is she now?"

The doctor looked at him and opened his mouth as if to answer, and closed it. "She is being held at Starfleet medical under armed guard. She will be, if this continues the focus of many tests, while they try to stop the virus."

Chakotay gave a mirthless laugh. "There's only one way to stop it isn't there? The same way we stopped Brenna Covington." More a statement than a question.

The doctor nodded grimly. "So what you're asking, is that I kill the one and only link I have left of the woman I love?"

Chakotay was totally taken aback by this. "I thought your holomatrix wouldn't allow you to kill an innocent?"

The doctor shook his head. "There are certain instances when even the most grounded and logical doctors have taken a life for the greater good."

He looked at the doctor once again, "Why didn't you do it, if you had access to her?"

"I was taken off the list of people allowed to see Marissa, the moment the child was born and the Admiral passed onto the other side, so to speak."

Chakotay looked to the doctor. "That's Kathryn's daughter's name. Marissa?"

The doctor nodded. "That was one thing she did get to do before she passed on. But I know there was also an encrypted padd left for you there. She said you'd know the passcode. That it was something that you'd used before and would use again but it would not be obvious or accessible to anyone else. I personally don't know what that is, or what it has to do with anything, but I know how much she meant to you and you meant to her. Who knows, that padd might hold the answer as to what to do with little Marissa." He paused, "I have to get going, I'm not even supposed to have any contact with you or with the other former members of Voyager's staff, especially the senior staff. I hope that all goes well, and I have to say I'm very sorry. We and the rest of the world have lost a great resource in Kathryn Janeway."

Chakotay looked at the doctor. "Thanks, Doc. I hope we can all figure this out."

Chakotay let the doctor out and went into the apartment. He went over to his console and looked up the location of B'Elanna and Tom Paris. He sent them a message. It simply said, We lost Admiral Janeway.

And the trouble has just begun.

TBC in part IX 


	10. Chapter 9

Part IX Rated: M

By: AW

Disclaimer: I don't own the people or the episodes but the story is mine.

In Confidence Part IX Rated: M

By: AW

Disclaimer: Blah blah blah blah, you all know what goes here.

The next day Chakotay made his way to Starfleet medical. He had made it all the way to the grounds of Starfleet Headquarters before he had turned around and taken off. He had ended up at a coffee shop just off the grounds, and had run into someone from his past.

"Hello, Harry."

Harry looked up at his Commanding Officer. "Commander."

Chakotay watched as Harry looked up at him, with the respect he still commanded from the former Voyager staff. "For now I am still a Commander. Some of us weren▓t lucky enough to get the promotion of their dreams; And you're what, 'Lieutenant Kim'?"

Harry shook his head. "Yes, sir; and I▓m sure you▓ll get the promotion soon enough"

He shook his head at the youthful pride that Harry still held. "You know Harry, you can call me Chakotay. You're not officially under my command any more, and I think we're off-duty."

Harry laughed, "I guess we are Chakotay." He looked at Chakotay; he looked lost, and there was a purpose he hadn't seen in him since Captain Janeway had brought him on board. "So how's the Admiral, Chakotay?"

Chakotay looked away, and realized how far he was out of the loop. "Well Harry, I'm going right now to see our daughter."

Harry's eyes bugged out of his head, and he looked at his former Commanding officer. "Well, congratulations Sir. I haven't seen the Captain since the promotion ceremony, I would love to see her."

Chakotay bowed his head. "I don't think that will be possible, Harry."

Harry looked at Chakotay. He paused, "When?"

Chakotay knew at that point that Harry had figured out some of what had happened. "About three days ago. She died in childbirth." Chakotay didn't feel the need to tell Harry anything more than that.

"I'm so sorry Chakotay. Would you like me to come with you to see your daughter?"

Chakotay just shook his head. "I don't think that'll be possible; Starfleet medical doesn't want people in the room seeing the baby until she's had a chance to adjust to me, and the fact that her mother isn't around." He paused, "You know, 'Delta Darling' dying in childbirth with her former maquis Commander's lovechild. The media isn't taking too kindly to that right now."

Harry just nodded. "I understand. Well I hope that we'll meet again soon Commander."

He watched Harry take off and went to Starfleet medical to meet his daughter.

Chakotay approached the door to Starfleet medical. He just stood there for a moment, not quite sure if he could go in there yet. Finally he gathered up all his strength and walked into the lab. He went right to Beverly Crusher's office. She would be able to tell him how to best proceed.

He was about to knock on the door when it opened and Dr. Crusher almost ran into him. "Doctor, I'm sorry. I was just..."

She looked at him. "Commander. We weren't sure we'd see you again. I mean after... and..."

Chakotay nodded. "Yes, well, I need to see that baby. Kathryn was, and will always be my soul mate. We just couldn't get it together while we were on Voyager. And I want to take responsibility for the child."

Crusher looked at the lost man in front of her. "She did leave the baby under your care. It seems that while you were on Voyager, you were both responsible for the other should anything happen and that agreement still stands."

Chakotay was shocked. He had heard it from Starfleet Command, and the EMH himself, but now it was real. "Okay well, when can I see the baby."

Doctor Crusher got a small smile on her face. "Well it was a girl, and Kathryn did name her before she passed. So you can see 'Marissa' soon, but before we do that, I do need to inform you that she left a note for you. It's got an encryption on it and she said you'd know what it was."

Chakotay nodded his head. "I understand, but can I see Marissa, then I'll take the note home and review it, home with my baby girl."

The doctor hesitated. "Well, I can't let the baby leave Starfleet medical, but you can take the note after you see the child."

Chakotay was frustrated. "What do you mean I can't take the baby home? Kathryn left her in my care."

Crusher just looked at him. "I'm sorry I can't let the baby go home with you, but you can see her now if you'd like." Crusher handed the padd to Chakotay and led him into the makeshift nursery.

Chakotay followed Doctor Crusher into the medical bay, and saw a small bassinette hiding in the corner. He followed her up to the small cubicle and looked down to see a small child.

As he looked into the bassinette he realized the child looked quite bit older than five days. He turned to Crusher, "She looks a whole lot older than a week."

Crusher nodded her head. "I know, and we're not sure if it▓s because of her mixed heritage or because of something the Borg programmed into her."

He noticed the red down on Marissa▓s head, and the small implant near her temple. Very similar to one of the ones that had adorned Seven's perfect skin. "Okay well when can I take her home than?"

She looked away. "I don't know Commander. We don't know what kind of threat she poses or if she is a threat to the Federation at all. I..."

Chakotay got angry. "Damn the Federation. She's a child, my child. The only thing I have left of the woman I love."

Crusher just sat silently and watched the damaged man in front of her. "You can pick her up you know."

Chakotay noticed her ignoring his questions and just scooped the child up. Crusher handed him a bottle, and he fed his daughter. An hour later he left Starfleet medical with a note that was hopefully an explanation.

He looked at the note for a good two hours before getting up the courage to open it and hear the explanation his love had given him. He checked out the number of letters and saw 12 letters knowing what it would be. He entered the word 'angrywarrior' and saw that it opened readily for him.

He read the letter. It began nicely, then it got worse...

TBC in part X 


	11. Chapter 10

In Confidence, Book I

Part X

Rated: M

By: AW Disclaimer: I don't own the people or the episodes but the story is mine.

Chakotay sat in the prison cell. He had been shipped off to New Zealand. He had been scheduled to spend the next five years here, that would make him 60 by the time he got out.

He was done.

He had left the message for Harry and hoped he understood the seriousness of his request. He had messaged Harry and Tom. Tom, he had told where to find him. He was too embarrassed to be put in front of Harry at this point.

B'Elanna had been kept in the dark. She did know of what he had done, she didn't have a choice, it was all over the news channels.

But what had to be done to ensure the safety of the Federation and a future for them all, was what Kathryn had requested of him. When Tom had heard this he had come.

"Hey old man, old habits die hard don't they?"

And so he had told Tom of everything. Of how hard it had been to let go of both Kathryn and Marissa. Of how the reason he had done what he had done was to stop the invasion that had started with Brenna Covington.

He had cried, in front of Tom Paris. He had finally let the flood gates open, and cried for all he had lost over the past year.

He had passed a message on to Harry to enter in the capsule that would one day, one time get to Kathryn, his Kathryn before everything changed.

He had told Tom of the reasons he had done what he had done. He had told Tom that if all went as it should be, The Paris' life should be unaffected.

He hoped anyway...but if things went as they should, life would only be changed to the point where they were on Quarren.  
But without Admiral Janeway, would they have the Borg technology that he needed and sought.

He looked to Tom. "Tom, you're a lieutenant Commander now, I need you to pursue the Borg technology that Admiral Janeway would have discovered had she lived through her whole life."

Tom looked at him suspiciously, "You're not thinking..."

"I need to Tom, I have to fix things."

Tom nodded his head, "I guess you have to do what you have to do, but you're stuck here for..."

Chakotay cut him off, "Five years at which point I'm gonna need your help."

Paris nodded his head. "Good thing I respect you the way I do."

Chakotay laughed, "Good thing."

He looked to Tom, "I was going to leave you and B'Elanna both out of it, but I need to make sure that Harry gets it right, so you're going to have to help him. You have to keep B'Elanna in the dark. She's been through so much recently with her trip to Boreth and the death of her mother, I just couldn't put her through any more stress and pain then she has to be." He paused, "And she missed so much time with little Miral, just give her this time to get reaquainted with the little tyke." Tom nodded. "Okay, but it won't be easy, you know how nosy and pigheaded she can be."

Chakotay almost chuckled, "I have a vague idea."

Tom just smiled. "Well, I've been here, it▓s not that bad, just ride it out." He hesitated, "You did what you had to do Chakotay, whether anyone else believes it or not."

Chakotay watched as Paris parted his company, and he waited... he just hoped he lasted that long and still believed in what he had to do after everything.

END PART X

END BOOK I


End file.
